7KQ8 | pdb_00007kq8

Structure of iron bound MEMO1

PDB DOI: https://doi.org/10.2210/pdb7KQ8/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-11-13 Released: 2021-11-17
Deposition Author(s): Boniecki, M.T., Uhlemann, E.E., Dmitriev, O.Y.
Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.202 (Depositor), 0.203 (DCC)
R-Value Work:
0.159 (Depositor), 0.161 (DCC)
R-Value Observed:
0.160 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

MEMO1 binds iron and modulates iron homeostasis in cancer cells.

Dolgova, N., Uhlemann, E.E., Boniecki, M.T., Vizeacoumar, F.S., Ara, A., Nouri, P., Ralle, M., Tonelli, M., Abbas, S.A., Patry, J., Elhasasna, H., Freywald, A., Vizeacoumar, F.J., Dmitriev, O.Y.

(2024) Elife 13

PubMed: 38640016 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.7554/eLife.86354
Primary Citation Related Structures:
7KQ8, 7L5C, 7M8H

PubMed Abstract:
Mediator of ERBB2-driven cell motility 1 (MEMO1) is an evolutionary conserved protein implicated in many biological processes; however, its primary molecular function remains unknown. Importantly, MEMO1 is overexpressed in many types of cancer and was shown to modulate breast cancer metastasis through altered cell motility. To better understand the function of MEMO1 in cancer cells, we analyzed genetic interactions of MEMO1 using gene essentiality data from 1028 cancer cell lines and found multiple iron-related genes exhibiting genetic relationships with MEMO1. We experimentally confirmed several interactions between MEMO1 and iron-related proteins in living cells, most notably, transferrin receptor 2 ( TFR 2), mitoferrin-2 ( SLC25A28 ), and the global iron response regulator IRP1 ( ACO1 ). These interactions indicate that cells with high-MEMO1 expression levels are hypersensitive to the disruptions in iron distribution. Our data also indicate that MEMO1 is involved in ferroptosis and is linked to iron supply to mitochondria. We have found that purified MEMO1 binds iron with high affinity under redox conditions mimicking intracellular environment and solved MEMO1 structures in complex with iron and copper. Our work reveals that the iron coordination mode in MEMO1 is very similar to that of iron-containing extradiol dioxygenases, which also display a similar structural fold. We conclude that MEMO1 is an iron-binding protein that modulates iron homeostasis in cancer cells.

Organizational Affiliation

Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Canada.

Macromolecule Content

Total Structure Weight: 138.42 kDa
Atom Count: 10,317
Modeled Residue Count: 1,176
Deposited Residue Count: 1,176
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein MEMO1	A, B, C, D	294	Homo sapiens	Mutation(s): 0 Gene Names: MEMO1, C2orf4, MEMO, NS5ATP7, CGI-27
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y316 (Homo sapiens) Explore Q9Y316 Go to UniProtKB: Q9Y316
PHAROS: Q9Y316 GTEx: ENSG00000162959
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9Y316
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GSH Query on GSH Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain LA [auth C] SDF format, chain V [auth B] SDF format, chain WA [auth D] MOL2 format, chain E [auth A] MOL2 format, chain LA [auth C] MOL2 format, chain V [auth B] MOL2 format, chain WA [auth D] mmCIF format, chain E [auth A] mmCIF format, chain LA [auth C] mmCIF format, chain V [auth B] mmCIF format, chain WA [auth D]	E [auth A], LA [auth C], V [auth B], WA [auth D]	Glutathione C₁₀ H₁₇ N₃ O₆ S RWSXRVCMGQZWBV-WDSKDSINSA-N		Interactions Focus chain E [auth A] Focus chain LA [auth C] Focus chain V [auth B] Focus chain WA [auth D] Interactions & Density Focus chain E [auth A] Focus chain LA [auth C] Focus chain V [auth B] Focus chain WA [auth D]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain GA [auth B] SDF format, chain PA [auth C] SDF format, chain QA [auth C] MOL2 format, chain GA [auth B] MOL2 format, chain PA [auth C] MOL2 format, chain QA [auth C] mmCIF format, chain GA [auth B] mmCIF format, chain PA [auth C] mmCIF format, chain QA [auth C]	GA [auth B], PA [auth C], QA [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain GA [auth B] Focus chain PA [auth C] Focus chain QA [auth C] Interactions & Density Focus chain GA [auth B] Focus chain PA [auth C] Focus chain QA [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain RA [auth C] SDF format, chain W [auth B] SDF format, chain XA [auth D] MOL2 format, chain RA [auth C] MOL2 format, chain W [auth B] MOL2 format, chain XA [auth D] mmCIF format, chain RA [auth C] mmCIF format, chain W [auth B] mmCIF format, chain XA [auth D]	RA [auth C], W [auth B], XA [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain RA [auth C] Focus chain W [auth B] Focus chain XA [auth D] Interactions & Density Focus chain RA [auth C] Focus chain W [auth B] Focus chain XA [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain AB [auth D] SDF format, chain BA [auth B] SDF format, chain BB [auth D] SDF format, chain CA [auth B] SDF format, chain CB [auth D] SDF format, chain DA [auth B] SDF format, chain DB [auth D] SDF format, chain EA [auth B] SDF format, chain EB [auth D] SDF format, chain F [auth A] SDF format, chain FA [auth B] SDF format, chain FB [auth D] SDF format, chain G [auth A] SDF format, chain GB [auth D] SDF format, chain H [auth A] SDF format, chain HA [auth B] SDF format, chain I [auth A] SDF format, chain IA [auth B] SDF format, chain J [auth A] SDF format, chain JA [auth B] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain MA [auth C] SDF format, chain N [auth A] SDF format, chain NA [auth C] SDF format, chain O [auth A] SDF format, chain OA [auth C] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain SA [auth C] SDF format, chain T [auth A] SDF format, chain TA [auth C] SDF format, chain UA [auth C] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain YA [auth D] SDF format, chain Z [auth B] SDF format, chain ZA [auth D] MOL2 format, chain AA [auth B] MOL2 format, chain AB [auth D] MOL2 format, chain BA [auth B] MOL2 format, chain BB [auth D] MOL2 format, chain CA [auth B] MOL2 format, chain CB [auth D] MOL2 format, chain DA [auth B] MOL2 format, chain DB [auth D] MOL2 format, chain EA [auth B] MOL2 format, chain EB [auth D] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain FB [auth D] MOL2 format, chain G [auth A] MOL2 format, chain GB [auth D] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth B] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth B] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth B] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth C] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth C] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth C] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth C] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth C] MOL2 format, chain UA [auth C] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain YA [auth D] MOL2 format, chain Z [auth B] MOL2 format, chain ZA [auth D] mmCIF format, chain AA [auth B] mmCIF format, chain AB [auth D] mmCIF format, chain BA [auth B] mmCIF format, chain BB [auth D] mmCIF format, chain CA [auth B] mmCIF format, chain CB [auth D] mmCIF format, chain DA [auth B] mmCIF format, chain DB [auth D] mmCIF format, chain EA [auth B] mmCIF format, chain EB [auth D] mmCIF format, chain F [auth A] mmCIF format, chain FA [auth B] mmCIF format, chain FB [auth D] mmCIF format, chain G [auth A] mmCIF format, chain GB [auth D] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth B] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth B] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth B] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth C] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth C] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth C] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain SA [auth C] mmCIF format, chain T [auth A] mmCIF format, chain TA [auth C] mmCIF format, chain UA [auth C] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain YA [auth D] mmCIF format, chain Z [auth B] mmCIF format, chain ZA [auth D]	AA [auth B] AB [auth D] BA [auth B] BB [auth D] CA [auth B] AA [auth B], AB [auth D], BA [auth B], BB [auth D], CA [auth B], CB [auth D], DA [auth B], DB [auth D], EA [auth B], EB [auth D], F [auth A], FA [auth B], FB [auth D], G [auth A], GB [auth D], H [auth A], HA [auth B], I [auth A], IA [auth B], J [auth A], JA [auth B], K [auth A], L [auth A], M [auth A], MA [auth C], N [auth A], NA [auth C], O [auth A], OA [auth C], P [auth A], Q [auth A], R [auth A], S [auth A], SA [auth C], T [auth A], TA [auth C], UA [auth C], X [auth B], Y [auth B], YA [auth D], Z [auth B], ZA [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain AB [auth D] Focus chain BA [auth B] Focus chain BB [auth D] Focus chain CA [auth B] Focus chain CB [auth D] Focus chain DA [auth B] Focus chain DB [auth D] Focus chain EA [auth B] Focus chain EB [auth D] Focus chain F [auth A] Focus chain FA [auth B] Focus chain FB [auth D] Focus chain G [auth A] Focus chain GB [auth D] Focus chain H [auth A] Focus chain HA [auth B] Focus chain I [auth A] Focus chain IA [auth B] Focus chain J [auth A] Focus chain JA [auth B] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain MA [auth C] Focus chain N [auth A] Focus chain NA [auth C] Focus chain O [auth A] Focus chain OA [auth C] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain SA [auth C] Focus chain T [auth A] Focus chain TA [auth C] Focus chain UA [auth C] Focus chain X [auth B] Focus chain Y [auth B] Focus chain YA [auth D] Focus chain Z [auth B] Focus chain ZA [auth D] Interactions & Density Focus chain AA [auth B] Focus chain AB [auth D] Focus chain BA [auth B] Focus chain BB [auth D] Focus chain CA [auth B] Focus chain CB [auth D] Focus chain DA [auth B] Focus chain DB [auth D] Focus chain EA [auth B] Focus chain EB [auth D] Focus chain F [auth A] Focus chain FA [auth B] Focus chain FB [auth D] Focus chain G [auth A] Focus chain GB [auth D] Focus chain H [auth A] Focus chain HA [auth B] Focus chain I [auth A] Focus chain IA [auth B] Focus chain J [auth A] Focus chain JA [auth B] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain MA [auth C] Focus chain N [auth A] Focus chain NA [auth C] Focus chain O [auth A] Focus chain OA [auth C] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain SA [auth C] Focus chain T [auth A] Focus chain TA [auth C] Focus chain UA [auth C] Focus chain X [auth B] Focus chain Y [auth B] Focus chain YA [auth D] Focus chain Z [auth B] Focus chain ZA [auth D]
FE2 (Subject of Investigation/LOI) Query on FE2 Download:Ideal Coordinates CCD File SDF format, chain HB [auth D] SDF format, chain KA [auth B] SDF format, chain U [auth A] SDF format, chain VA [auth C] MOL2 format, chain HB [auth D] MOL2 format, chain KA [auth B] MOL2 format, chain U [auth A] MOL2 format, chain VA [auth C] mmCIF format, chain HB [auth D] mmCIF format, chain KA [auth B] mmCIF format, chain U [auth A] mmCIF format, chain VA [auth C]	HB [auth D], KA [auth B], U [auth A], VA [auth C]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N		Interactions Focus chain HB [auth D] Focus chain KA [auth B] Focus chain U [auth A] Focus chain VA [auth C] Interactions & Density Focus chain HB [auth D] Focus chain KA [auth B] Focus chain U [auth A] Focus chain VA [auth C]

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002593 (GSH) Query on PRD_002593	E [auth A], LA [auth C], V [auth B], WA [auth D]	Glutathione	Peptide-like / Oxidation-reduction		Interactions Focus chain E [auth A] Focus chain LA [auth C] Focus chain V [auth B] Focus chain WA [auth D] Interactions & Density Focus chain E [auth A] Focus chain LA [auth C] Focus chain V [auth B] Focus chain WA [auth D]